Priority index

Date: 2021_03_18

Analyzed by: Sara Saez Atienzar

Background

Priority index is designed to discover and prioritize drug targets at the gene and pathway level. Taking as inputs GWAS summary statistics for immune-related traits/diseases, Pi uses genomic predictors to identify and score genomic seed genes likely responsible for these genetic associations, including nearby genes nGene based on genomic proximity and genomic organisation; chromatin conformation genes cGene based on summary data produced from promoter capture Hi-C studies; and expression-associated genes eGene based on summary data produced from eQTL mapping.

Information about Priority Index can be found at: http://pi314.r-forge.r-project.org Citation Hai Fang, The ULTRA-DD Consortium, Julian C Knight. Pi: an R/Bioconductor package leveraging genetic evidence to prioritise drug targets at the gene and pathway level. Bioconductor (2020); doi:10.18129/B9.bioc.Pi

Get the GWAS input ready for the analysis It is essential to format the GWAS summary Stats. in a format that is readable by the software. This should include:

  1. rsID number (or positions in hg19, but this second option can be problematic)
  2. A column of suggestive values. This list is based on the p-value of the association and it will be FALSE for pvalues < 5e-8, otherwise, it will be TRUE.
  3. beta (effect allele), se and p-value of the association.
  4. Effect allele and other allele

Directory and organization

Priority Index Analysis

Formatting GWAS

PI as R script

Results top 30 prioritized genes

Drugs targetting the most druggable genes from the top30

How these results are different from the previous version?

Create a new folder with just the final results for Ruth